Genetically modified (GM) papaya (Carica papaya L.) line 55-1 (55-1), which is resistant to papaya ringspot virus infection, has been marketed internationally. Many countries such as the European Union, Japan, and Korea have a mandatory safety assessment, approval and labeling regulations for GM foods. Thus, there is a need for specific methods for detecting 55-1. In this study, we established a real-time PCR detection method applicable to 55-1 for a variety of papaya products. The limit of detection was possible for fresh papaya fruit up to dilutions of 0.005% and 0.01% (weight per weight [w/w]) for homozygous SunUp and heterozygous Rainbow cultivars, respectively, in non-GM papaya. The 55-1 event-specific detection method observed parallelism (r2>0.99) between the concentration of line 55-1 cultivars and Ct values obtained in amplification plots at concentrations of 0.005-10% for SunUp DNA and 0.01-10% for Rainbow DNA. The method was applicable to the qualitative detection in various types of processed products (cocktail fruit, dried fruit, juice, etc.) containing papaya as a main ingredient. Monitoring papaya products for the presence of GM papaya were demonstrated using a P35S and T-nos real-time PCR detection method but no amplification signals were detected.